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. 2019 Dec 18;6(6):064704. doi: 10.1063/1.5132692

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© 2019 Author(s).

2329-7778/2019/6(6)/064704/11

All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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FIG. 5. — Dependence of covariance on distance for only intraprotein Cα atom pairs. Mean values of covariance ± standard errors from the MD simulations are shown using vertically oriented error bars. Values computed from RBM models are shown using dashed lines (standard errors are O(10⁻⁵) Å² and are therefore not shown). The upper y-range is truncated at 0.6 Å², showing the full range of the exponential fit but excluding one high covariance value at the shortest distance from the MD values in each panel. Left: AMBER force field. The RBM model has a width (SD) 0.95° for the angular distribution and 0.24 Å for the translational distribution. Right: CHARMM force field. The RBM model has a width (SD) 1.05° for the angular distribution and 0.27 Å for the translational distribution. The MD simulations are well modeled using rigid-body translations and rotations for distances greater than 20 Å.